Job ID = 14159185 SRX = SRX9120616 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28295530 spots for SRR12638559/SRR12638559.sra Written 28295530 spots for SRR12638559/SRR12638559.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159425 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:38 28295530 reads; of these: 28295530 (100.00%) were unpaired; of these: 89597 (0.32%) aligned 0 times 23608487 (83.44%) aligned exactly 1 time 4597446 (16.25%) aligned >1 times 99.68% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4647253 / 28205933 = 0.1648 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 08 Dec 2021 20:20:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:20:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:20:55: 1000000 INFO @ Wed, 08 Dec 2021 20:21:00: 2000000 INFO @ Wed, 08 Dec 2021 20:21:05: 3000000 INFO @ Wed, 08 Dec 2021 20:21:10: 4000000 INFO @ Wed, 08 Dec 2021 20:21:15: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 08 Dec 2021 20:21:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:21:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:21:20: 6000000 INFO @ Wed, 08 Dec 2021 20:21:26: 1000000 INFO @ Wed, 08 Dec 2021 20:21:26: 7000000 INFO @ Wed, 08 Dec 2021 20:21:32: 2000000 INFO @ Wed, 08 Dec 2021 20:21:32: 8000000 INFO @ Wed, 08 Dec 2021 20:21:37: 3000000 INFO @ Wed, 08 Dec 2021 20:21:37: 9000000 INFO @ Wed, 08 Dec 2021 20:21:43: 4000000 INFO @ Wed, 08 Dec 2021 20:21:43: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 20:21:49: 5000000 INFO @ Wed, 08 Dec 2021 20:21:49: 11000000 INFO @ Wed, 08 Dec 2021 20:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 08 Dec 2021 20:21:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:21:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:21:55: 6000000 INFO @ Wed, 08 Dec 2021 20:21:55: 12000000 INFO @ Wed, 08 Dec 2021 20:21:57: 1000000 INFO @ Wed, 08 Dec 2021 20:22:01: 7000000 INFO @ Wed, 08 Dec 2021 20:22:01: 13000000 INFO @ Wed, 08 Dec 2021 20:22:04: 2000000 INFO @ Wed, 08 Dec 2021 20:22:07: 8000000 INFO @ Wed, 08 Dec 2021 20:22:07: 14000000 INFO @ Wed, 08 Dec 2021 20:22:11: 3000000 INFO @ Wed, 08 Dec 2021 20:22:13: 9000000 INFO @ Wed, 08 Dec 2021 20:22:14: 15000000 INFO @ Wed, 08 Dec 2021 20:22:18: 4000000 INFO @ Wed, 08 Dec 2021 20:22:19: 10000000 INFO @ Wed, 08 Dec 2021 20:22:20: 16000000 INFO @ Wed, 08 Dec 2021 20:22:24: 5000000 INFO @ Wed, 08 Dec 2021 20:22:26: 11000000 INFO @ Wed, 08 Dec 2021 20:22:26: 17000000 INFO @ Wed, 08 Dec 2021 20:22:31: 6000000 INFO @ Wed, 08 Dec 2021 20:22:32: 12000000 INFO @ Wed, 08 Dec 2021 20:22:32: 18000000 INFO @ Wed, 08 Dec 2021 20:22:38: 7000000 INFO @ Wed, 08 Dec 2021 20:22:38: 13000000 INFO @ Wed, 08 Dec 2021 20:22:38: 19000000 INFO @ Wed, 08 Dec 2021 20:22:44: 14000000 INFO @ Wed, 08 Dec 2021 20:22:45: 20000000 INFO @ Wed, 08 Dec 2021 20:22:45: 8000000 INFO @ Wed, 08 Dec 2021 20:22:51: 15000000 INFO @ Wed, 08 Dec 2021 20:22:51: 21000000 INFO @ Wed, 08 Dec 2021 20:22:52: 9000000 INFO @ Wed, 08 Dec 2021 20:22:57: 22000000 INFO @ Wed, 08 Dec 2021 20:22:57: 16000000 INFO @ Wed, 08 Dec 2021 20:22:58: 10000000 INFO @ Wed, 08 Dec 2021 20:23:03: 23000000 INFO @ Wed, 08 Dec 2021 20:23:03: 17000000 INFO @ Wed, 08 Dec 2021 20:23:05: 11000000 INFO @ Wed, 08 Dec 2021 20:23:07: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:23:07: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:23:07: #1 total tags in treatment: 23558680 INFO @ Wed, 08 Dec 2021 20:23:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:23:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:23:07: #1 tags after filtering in treatment: 23558680 INFO @ Wed, 08 Dec 2021 20:23:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:23:07: #1 finished! INFO @ Wed, 08 Dec 2021 20:23:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:23:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:23:08: #2 number of paired peaks: 148 WARNING @ Wed, 08 Dec 2021 20:23:08: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Wed, 08 Dec 2021 20:23:08: start model_add_line... INFO @ Wed, 08 Dec 2021 20:23:09: start X-correlation... INFO @ Wed, 08 Dec 2021 20:23:09: end of X-cor INFO @ Wed, 08 Dec 2021 20:23:09: #2 finished! INFO @ Wed, 08 Dec 2021 20:23:09: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:23:09: #2 alternative fragment length(s) may be 1,24,42,525,540,553 bps INFO @ Wed, 08 Dec 2021 20:23:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_model.r WARNING @ Wed, 08 Dec 2021 20:23:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:23:09: #2 You may need to consider one of the other alternative d(s): 1,24,42,525,540,553 WARNING @ Wed, 08 Dec 2021 20:23:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:23:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:23:09: 18000000 INFO @ Wed, 08 Dec 2021 20:23:12: 12000000 INFO @ Wed, 08 Dec 2021 20:23:15: 19000000 INFO @ Wed, 08 Dec 2021 20:23:19: 13000000 INFO @ Wed, 08 Dec 2021 20:23:22: 20000000 INFO @ Wed, 08 Dec 2021 20:23:25: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:23:28: 21000000 INFO @ Wed, 08 Dec 2021 20:23:32: 15000000 INFO @ Wed, 08 Dec 2021 20:23:34: 22000000 INFO @ Wed, 08 Dec 2021 20:23:39: 16000000 INFO @ Wed, 08 Dec 2021 20:23:40: 23000000 INFO @ Wed, 08 Dec 2021 20:23:44: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:23:44: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:23:44: #1 total tags in treatment: 23558680 INFO @ Wed, 08 Dec 2021 20:23:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:23:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:23:44: #1 tags after filtering in treatment: 23558680 INFO @ Wed, 08 Dec 2021 20:23:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:23:44: #1 finished! INFO @ Wed, 08 Dec 2021 20:23:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:23:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:23:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:23:45: #2 number of paired peaks: 148 WARNING @ Wed, 08 Dec 2021 20:23:45: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Wed, 08 Dec 2021 20:23:45: start model_add_line... INFO @ Wed, 08 Dec 2021 20:23:46: start X-correlation... INFO @ Wed, 08 Dec 2021 20:23:46: end of X-cor INFO @ Wed, 08 Dec 2021 20:23:46: #2 finished! INFO @ Wed, 08 Dec 2021 20:23:46: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:23:46: #2 alternative fragment length(s) may be 1,24,42,525,540,553 bps INFO @ Wed, 08 Dec 2021 20:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_model.r WARNING @ Wed, 08 Dec 2021 20:23:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:23:46: #2 You may need to consider one of the other alternative d(s): 1,24,42,525,540,553 WARNING @ Wed, 08 Dec 2021 20:23:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:23:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:23:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:23:46: 17000000 INFO @ Wed, 08 Dec 2021 20:23:52: 18000000 INFO @ Wed, 08 Dec 2021 20:23:59: 19000000 INFO @ Wed, 08 Dec 2021 20:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_summits.bed INFO @ Wed, 08 Dec 2021 20:24:00: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:24:05: 20000000 INFO @ Wed, 08 Dec 2021 20:24:12: 21000000 INFO @ Wed, 08 Dec 2021 20:24:18: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:24:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:24:25: 23000000 INFO @ Wed, 08 Dec 2021 20:24:28: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:24:28: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:24:28: #1 total tags in treatment: 23558680 INFO @ Wed, 08 Dec 2021 20:24:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:24:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:24:29: #1 tags after filtering in treatment: 23558680 INFO @ Wed, 08 Dec 2021 20:24:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:24:29: #1 finished! INFO @ Wed, 08 Dec 2021 20:24:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:24:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:24:30: #2 number of paired peaks: 148 WARNING @ Wed, 08 Dec 2021 20:24:30: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Wed, 08 Dec 2021 20:24:30: start model_add_line... INFO @ Wed, 08 Dec 2021 20:24:30: start X-correlation... INFO @ Wed, 08 Dec 2021 20:24:30: end of X-cor INFO @ Wed, 08 Dec 2021 20:24:30: #2 finished! INFO @ Wed, 08 Dec 2021 20:24:30: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:24:30: #2 alternative fragment length(s) may be 1,24,42,525,540,553 bps INFO @ Wed, 08 Dec 2021 20:24:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_model.r WARNING @ Wed, 08 Dec 2021 20:24:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:24:30: #2 You may need to consider one of the other alternative d(s): 1,24,42,525,540,553 WARNING @ Wed, 08 Dec 2021 20:24:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:24:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:24:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_summits.bed INFO @ Wed, 08 Dec 2021 20:24:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:25:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_summits.bed INFO @ Wed, 08 Dec 2021 20:25:20: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling